I’m new to atom, migrating from TextMate . So far I’m generally happy. One thing that bugs me is that the line numbers are not aligned to the lines of code to which they are associated. Is this normal? Is there a way to fix it?

Yup, it was my theme. I was using ‘Twilight Textmate’. I switched to plain old ‘Twilight’ and it is fine. I did prefer some things about ‘Twilight Textmate’, namely that it isn’t so bright. I guess I’ll have to figure out how to tweak such thing m’self. Thanks for the suggestion.